title: Culture-based diagnostic microbiology in cystic fibrosis: can we simplify the complexity?
abstract: Cystic fibrosis (CF) diagnostic microbiology has evolved from a focus on Staphylococcus aureus as primary pathogen to identification of the contribution of Pseudomonas aeruginosa and other non-fermenting gram negatives; studies of the lung microbiome have added new complexity. This review summarizes state-of-the art culture methods and makes recommendations for addition of non-culture based methods in the diagnostic laboratory. Plating on selective media is recommended, with organism identification by matrix assisted laser desorption-time of flight mass spectroscopy and real-time polymerase chain reaction (PCR) supplanting both biochemical identification and other less accurate and more time-consuming molecular methods. Conventional antibiotic susceptibility testing, possibly at less frequent intervals, remains the standard but more CF-relevant methods may arise in the future. There is a role for direct identification of organisms in clinical samples using quantitative real-time PCR, next generation sequencing, and metagenomic studies for the re-examination of samples that do not yield traditional CF pathogens.
authors.affiliation: Seattle Children's Hospital, University of Washington School of Medicine, Department of Pediatrics, Division of Infectious Diseases, Seattle, WA, USA. Electronic address: jane.burns@seattlechildrens.org.
authors.forename: Jane L
authors.initials: JL
authors.lastname: Burns
authors.affiliation: Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), CNRS-IRD UMR 6236, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille-Université, Marseille, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Rolain
mesh_terms: D003550:Cystic Fibrosis / Q000382:microbiology*; D006801:Humans; D008172:Lung Diseases, Fungal / Q000175:diagnosis* / Q000382:microbiology*; D008828:Microbiological Techniques / Q000379:methods*; D018410:Pneumonia, Bacterial / Q000175:diagnosis* / Q000382:microbiology*; D060888:Real-Time Polymerase Chain Reaction
keywords: Bacteria; Microbiology; Susceptibility testing